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(-) Description

Title :  CRYSTAL STRUCTURE OF ESCHERICHIA COLI TRYPTOPHANASE PURIFIED FROM ALKALINE STRESSED BACTERIAL CULTURE.
 
Authors :  S. Rety, P. Deschamps, N. Leulliot
Date :  11 Jun 14  (Deposition) - 24 Jun 15  (Release) - 11 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.78
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Lyase, Alkaline Stress, Protein Purification (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Rety, P. Deschamps, N. Leulliot
Structure Of Escherichia Coli Tryptophanase Purified From An Alkaline-Stressed Bacterial Culture.
Acta Crystallogr. , Sect. F V. 71 1378 2015
PubMed-ID: 26527264  |  Reference-DOI: 10.1107/S2053230X15017549

(-) Compounds

Molecule 1 - TRYPTOPHANASE
    Chains: A, B, C, D
    EC Number: 4.1.99.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA 2
    Fragment: RESIDUES 6-476
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: L-TRYPTOPHAN INDOLE-LYASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 29)

Asymmetric Unit (2, 29)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2SO428Ligand/IonSULFATE ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1BME-1Ligand/IonBETA-MERCAPTOETHANOL
2SO46Ligand/IonSULFATE ION
Biological Unit 2 (2, 9)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2SO48Ligand/IonSULFATE ION
Biological Unit 3 (1, 8)
No.NameCountTypeFull Name
1BME-1Ligand/IonBETA-MERCAPTOETHANOL
2SO48Ligand/IonSULFATE ION
Biological Unit 4 (1, 6)
No.NameCountTypeFull Name
1BME-1Ligand/IonBETA-MERCAPTOETHANOL
2SO46Ligand/IonSULFATE ION

(-) Sites  (29, 29)

Asymmetric Unit (29, 29)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:54 , GLN A:101 , GLY A:102 , ARG A:103 , SER A:267 , LYS A:269BINDING SITE FOR RESIDUE SO4 A1469
02AC2SOFTWAREGLU A:72 , LEU A:310 , SER B:54 , GLY B:55 , PRO B:275BINDING SITE FOR RESIDUE SO4 A1470
03AC3SOFTWAREVAL A:388 , ALA A:389 , PHE A:434 , GLU A:437 , ALA A:438BINDING SITE FOR RESIDUE SO4 A1471
04AC4SOFTWAREMET A:1 , VAL C:388 , ALA C:389 , PHE C:434 , GLU C:437 , ALA C:438BINDING SITE FOR RESIDUE SO4 C1455
05AC5SOFTWARETHR A:23 , ARG A:24BINDING SITE FOR RESIDUE SO4 A1472
06AC6SOFTWAREALA A:84 , GLN A:94 , HOH A:2018 , HOH A:2039BINDING SITE FOR RESIDUE SO4 A1473
07AC7SOFTWARETHR A:52 , ASP A:53 , LYS A:270 , ARG A:419BINDING SITE FOR RESIDUE SO4 A1474
08AC8SOFTWAREGLY A:55 , PRO A:275 , GLU B:72 , LEU B:310BINDING SITE FOR RESIDUE SO4 B1454
09AC9SOFTWARETRP B:248 , GLN B:252 , HOH B:2029BINDING SITE FOR RESIDUE SO4 B1455
10BC1SOFTWARETYR B:74 , TYR B:307BINDING SITE FOR RESIDUE SO4 B1456
11BC2SOFTWARETYR B:307 , HOH B:2030 , HOH B:2031BINDING SITE FOR RESIDUE SO4 B1457
12BC3SOFTWAREGLY B:102 , ARG B:103 , SER B:267 , LYS B:269BINDING SITE FOR RESIDUE SO4 B1458
13BC4SOFTWAREGLU B:2 , VAL D:388 , ALA D:389 , PHE D:434 , GLU D:437 , ALA D:438BINDING SITE FOR RESIDUE SO4 D1455
14BC5SOFTWARETHR B:60 , SER B:62 , ASP B:324 , HOH B:2023 , PRO D:18BINDING SITE FOR RESIDUE SO4 B1459
15BC6SOFTWARETHR B:22 , THR B:23 , ARG B:24 , ARG B:27BINDING SITE FOR RESIDUE SO4 B1460
16BC7SOFTWARESER B:75 , GLY B:76BINDING SITE FOR RESIDUE BME B1461
17BC8SOFTWAREGLN C:101 , GLY C:102 , ARG C:103 , SER C:267 , LYS C:269BINDING SITE FOR RESIDUE SO4 C1456
18BC9SOFTWARETHR C:52 , LYS C:270BINDING SITE FOR RESIDUE SO4 C1457
19CC1SOFTWARETHR C:22 , THR C:23 , ARG C:24 , ARG C:27 , HOH C:2004 , HOH C:2024BINDING SITE FOR RESIDUE SO4 C1458
20CC2SOFTWAREGLU C:72 , SER D:54 , GLY D:55 , LYS D:269 , PRO D:275BINDING SITE FOR RESIDUE SO4 D1456
21CC3SOFTWAREGLN C:94 , HOH C:2011BINDING SITE FOR RESIDUE SO4 C1459
22CC4SOFTWARESER C:398BINDING SITE FOR RESIDUE SO4 C1460
23CC5SOFTWARELYS B:211 , LYS C:211 , GLU C:244 , TYR C:245 , GLU C:256BINDING SITE FOR RESIDUE SO4 C1461
24CC6SOFTWAREPRO C:414BINDING SITE FOR RESIDUE SO4 C1462
25CC7SOFTWARESER C:54 , GLY C:55 , GLU D:72 , ALA D:73BINDING SITE FOR RESIDUE SO4 D1457
26CC8SOFTWAREGLN D:101 , GLY D:102 , ARG D:103 , SER D:267 , LYS D:269BINDING SITE FOR RESIDUE SO4 D1458
27CC9SOFTWAREGLN C:101 , LEU D:310BINDING SITE FOR RESIDUE SO4 D1459
28DC1SOFTWARELEU D:452 , THR D:453BINDING SITE FOR RESIDUE SO4 D1460
29DC2SOFTWAREVAL B:388 , PHE B:434 , GLU B:437 , ALA B:438 , GLU D:2BINDING SITE FOR RESIDUE SO4 B1462

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4UP2)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ile A:195 -Thr A:196
2Phe B:288 -Asp B:289
3Ile D:195 -Thr D:196

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4UP2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4UP2)

(-) Exons   (0, 0)

(no "Exon" information available for 4UP2)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:420
                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeeeeeee....hhhhhhhhhhhh..hhhhhhhhhh.ee.........eehhhhhhhhh.......hhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhh.........eee.....eee...................hhhhhhhhhhhhhhhhh..eeee...........hhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhh.......hhhhhhhhhhhhh.eeeee..........eeeee........hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...eeee....eeeehhhhh...hhhhhhhhhhhhhhhhhhhee........eeee.......hhhhhhhhhhhhhhhhhhhhhh................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4up2 A   1 MENFKHLPEPFRIRVIEPVKRTTRAYREEAIIKSGMNPFLLDSEDVFIDLLTDSGTGAVTQSMQAAMMRGDEAYSGSRSYYALAESVKNIFGYQYTIPTHQGRGAEQIYIPVLIKKREQEKGLDRSKMVAFSNYFCTVRNVYIKEAFDTGVRYDFKGNFDLEGLERGIEEVGPNNVPYIVATITSNSAGGQPVSLANLKAMYSIAKKYDIPVVMDSARFAENAYFIKQREAEYKDWTIEQITRETYKYADMLAMSAKKDAMVPMGGLLCMKDDSFFGLEGGAMERLAVGLYDGMNLDWLAYRIAQVQYLVDGLEEIGVVCQQAGGHAAFVDAGKLLPHIPADQFPAQALACELYKVAGIRAVEIGPAELLRLTIPRATYTQTHMDFIIEAFKHVKENASNIKGLTFTYEPKVLRHFTAKL 468
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    || 152       162       172       182       192       202       212       222       232       242       252       262       272       282     ||312       322       332       342       352       362       372       382       392    || 418       428       438       448       458       468
                                                                                                                                                                135|                                                                                                                                         288|                                                                                     397|                                                      
                                                                                                                                                                 148                                                                                                                                          309                                                                                      414                                                      


Chain B from PDB  Type:PROTEIN  Length:408
                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeeeeee....hhhhhhhhhhhh..hhhhhhhhhh.ee.........eehhhhhhhhhh......hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhh........eee.....eee...................hhhhhhhhhhhhhhhhh..eeee...hhhhh...hhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhh.......hhhhhhhhhhhhh.eeeee..........eeeee...........hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...eeee....eeeehhhhh...hhhhhhhhhhhhhhhhhhhee.........eeee.......hhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4up2 B   2 ENFKHLPEPFRIRVIEPVKRTTRAYREEAIIKSGMNPFLLDSEDVFIDLLTDSGTGAVTQSMQAAMMRGDEAYSGSRSYYALAESVKNIFGYQYTIPTHQGRGAEQIYIPVLIKKREQEKGLDRSKMVAFSNYFCTVRNVYIKEAFDTGVRYDFKGNFDLEGLERGIEEVGPNNVPYIVATITSNSAGGQPVSLANLKAMYSIAKKYDIPVVMDSARFAENAYFIKQREAEYKDWTIEQITRETYKYADMLAMSAKKDAMVPMGGLLCMKDDSFFDYGGLEGGAMERLAVGLYDGMNLDWLAYRIAQVQYLVDGLEEIGVVCQQAGGHAAFVDAGKLLPHIPADQFPAQALACELYKVAGIRAVEIGSFAELLRLTIPRATYTQTHMDFIIEAFKHVKENASNIKGLT 453
                                    11        21        31        41        51        61        71        81        91       101       111       121       131   ||  153       163       173       183       193       203       213       223       233       243       253       263       273       283     ||310       320       330       340       350       360       370       380       390       415       425       435       445        
                                                                                                                                                               135|                                                                                                                                          289|                                                                                         399|                                      
                                                                                                                                                                148                                                                                                                                           307                                                                                          415                                      


Chain C from PDB  Type:PROTEIN  Length:404
                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeee.....hhhhhhhhhhh..hhhhhhhhhh.ee.........eehhhhhhhhhh......hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhh.........eee.....eee...................hhhhhhhhhhhhhhhhh..eeee...hhhhh...hhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.eeeee..........eeeee........hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...eeee....eeeehhhhh...hhhhhhhhhhhhhhhhhhhee.........eeee.......hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4up2 C   4 FKHLPEPFRIRVIEPVKRTTRAYREEAIIKSGMNPFLLDSEDVFIDLLTDSGTGAVTQSMQAAMMRGDEAYSGSRSYYALAESVKNIFGYQYTIPTHQGRGAEQIYIPVLIKKREQEKGLDRSKMVAFSNYFFTVRNVYIKEAFDTGVRYDFKGNFDLEGLERGIEEVGPNNVPYIVATITSNSAGGQPVSLANLKAMYSIAKKYDIPVVMDSARFAENAYFIKQREAEYKDWTIEQITRETYKYADMLAMSAKKDAMVPMGGLLCMKDDSFFGLEGGAMERLAVGLYDGMNLDWLAYRIAQVQYLVDGLEEIGVVCQQAGGHAAFVDAGKLLPHIPADQFPAQALACELYKVAGIRAVEIGSPAELLRLTIPRATYTQTHMDFIIEAFKHVKENASNIKGLTF 454
                                    13        23        33        43        53        63        73        83        93       103       113       123       133  ||   155       165       175       185       195       205       215       225       235       245       255       265       275       285  ||   315       325       335       345       355       365       375       385       395  ||   420       430       440       450    
                                                                                                                                                              136|                                                                                                                                        288|                                                                                      398|                                        
                                                                                                                                                               149                                                                                                                                         309                                                                                       414                                        


Chain D from PDB  Type:PROTEIN  Length:397
                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeee....hhhhhhhhhhhh..hhhhhhhhhh.ee.........eehhhhhhhhhh......hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhhh.........ee.........................hhhhhhhhhhhhhhhhh..eeee...hhhhh...hhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhh.......hhhhhhhhhhhhh.eeeee..........eeeee......hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...eeee....eeeehhhhh...hhhhhhhhhhhhhhhhhhhee....eeee.......hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4up2 D   2 ENFKHLPEPFRIRVIEPVKRTTRAYREEAIIKSGMNPFLLDSEDVFIDLLTDSGTGAVTQSMQAAMMRGDEAYSGSRSYYALAESVKNIFGYQYTIPTHQGRGAEQIYIPVLIKKREQEKGLDRSKMVAFSNYFVRNVYIKEAFDTGVRYDFKGNFDLEGLERGIEEVGPNNVPYIVATITSNSAGGQPVSLANLKAMYSIAKKYDIPVVMDSARFAENAYFIKQREAEYKDWTIEQITRETYKYADMLAMSAKKDAMVPMGGLLCMKDDSFLEGGAMERLAVGLYDGMNLDWLAYRIAQVQYLVDGLEEIGVVCQQAGGHAAFVDAGKLLPHIPADQFPAQALACELYKVAGIRAVEELLRLTIPRATYTQTHMDFIIEAFKHVKENASNIKGLTF 454
                                    11        21        31        41        51        61        71        81        91       101       111       121       131   ||  155       165       175       185       195       205       215       225       235       245       255       265       275       285 ||    317       327       337       347       357       367       377       387       417       427       437       447       
                                                                                                                                                               135|                                                                                                                                      287|                                                                                  395|                                      
                                                                                                                                                                150                                                                                                                                       310                                                                                   416
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4UP2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4UP2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4UP2)

(-) Gene Ontology  (17, 25)

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 Related Entries

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        TNAA_ECOLI | P0A853: 2c44 2oqx 2v0y 2v1p 4w1y 4w4h 5d8g

(-) Related Entries Specified in the PDB File

4up1 CRYSTAL STRUCTURE OF NATIVE HUMAN THYMIDYLATE SYNTHASE IN ACTIVE FORM